Hercules has agreed to sell a prime, centrally located parcel to Safeway to build a grocery store, in a tentative deal fraught with ifs and caveats.

Under a purchase-and-sale agreement ratified by the City Council on Tuesday, Property Development Centers, a Safeway subsidiary, would pay almost $9.3 million, or $16 a square foot, for the 13.3-acre, bullet-shaped site bounded by San Pablo Avenue, Sycamore Avenue and Tsushima Street. The company also envisions a gas station on the site as well as stores and homes along Sycamore Avenue.

But the cost of undergrounding utilities and clearing the site, which has been used over the years to store dirt from construction projects elsewhere, will leave the city with net proceeds somewhere in excess of $5 million, according to a staff report by City Manager Steve Duran.

The Hercules Redevelopment Agency acquired the property from developer Penterra Poe Hercules LLC in 2007 for $14.5 million; the agency transferred it to the city in March 2011 in a package of four parcels valued at an aggregate $33.7 million.

The transfer of the four properties satisfied the bulk of a $34.9 million agency debt to the city stemming from loans and infrastructure improvements between 2002 and 2008.

Hercules officials have said they are confident that the transfer will not be subject to any “clawback” by the state pursuant to the California Supreme Court-approved liquidation of redevelopment agencies statewide. That’s because Hercules’ property transfer satisfied a debt, whereas similar transfers in other cities often did not involve any money or other consideration.

But there are other hurdles to building a Safeway store, notably a restriction put into the deed by Penterra’s predecessor, American Stores Inc., then-owner of Lucky stores, that prohibits grocery sales. The city is suing American Stores, Lucky Stores and Save Mart Supermarkets in Contra Costa Superior Court seeking to remove the deed restriction.

A Safeway store, combined with the gas station and other stores on the site, would throw off about $500,000 a year in sales taxes for Hercules, Duran estimated.

Under the agreement, Hercules could hold on to a slice of the property fronting Sycamore Avenue, with the price for the rest decreasing to $14 a square foot. Across the avenue lies Sycamore North, a half-finished, two-building complex that is supposed to have stores on the ground floor and three floors of apartments on top.

Responding to a question from Councilwoman Myrna de Vera, Property Development Centers’ chief operating officer, David Zylstra, said that Safeway’s vision is “significantly different” from Hercules’ original vision for the site.

Tom Lochner covers Berkeley and occasionally West Contra Costa County for the Bay Area News Group. Tom grew up in Western Europe. He was a translator for a patent law firm and an international bank in Manhattan, then a housing manager in the Bronx and Upper Manhattan, before moving to California to become a journalist.